I would avoid drilling holes in the boat if you can, plus if your boat is a lighter lay up and your transom is on the thinner side (wich it sounds like it is) I wouldnt do it.

Most guys get a longer ratcheting tie down and run from one side of the trailer to the other and go over the pump, that is what I do. And i'm super anal about my stuff, so I put wrap a rag around the tiedown where it actually touches the boat and pump. This method has worked like a charm for me and I see lots of other guys do it too.

I'd try it before blasting holes in your rig.

I would not drill holes in it to thin

using the boat deck to tie it down is a problem too.  It can scuff up the paint/gel and if it's as light as you say it is that can cause stress cracks in it just as easily as tie downs on a thin transom.  I'd go with the straps around the pump. Since you say it's set back run the straps over the suction piece, (under the cables), close to the transom to each side of the trailer. Never used tie downs on my Daytona just the bow eye.

I've been pinning the front only for 35 yrs no problems yet